Metastable hybridization-based DNA information storage to allow rapid and permanent erasure

Jangwon Kim,David Yu Zhang,Jin H Bae,Michael Baym

doi:10.1038/s41467-020-18842-6

Jangwon Kim, David Yu Zhang + Show 2 more

Open Access

https://doi.org/10.1038/s41467-020-18842-6

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Abstract

The potential of DNA as an information storage medium is rapidly growing due to advances in DNA synthesis and sequencing. However, the chemical stability of DNA challenges the complete erasure of information encoded in DNA sequences. Here, we encode information in a DNA information solution, a mixture of true message- and false message-encoded oligonucleotides, and enables rapid and permanent erasure of information. True messages are differentiated by their hybridization to a "truth marker” oligonucleotide, and only true messages can be read; binding of the truth marker can be effectively randomized even with a brief exposure to the elevated temperature. We show 8 separate bitmap images can be stably encoded and read after storage at 25 °C for 65 days with an average of over 99% correct information recall, which extrapolates to a half-life of over 15 years at 25 °C. Heating to 95 °C for 5 minutes, however, permanently erases the message.

Highlights

The potential of DNA as an information storage medium is rapidly growing due to advances in DNA synthesis and sequencing
The cost of writing and reading information in DNA exceeds that of conventional methods such as flash drives and tape by many orders of magnitude[7], but biomedical research in genomics and synthetic biology are resulting in exponentially decreasing prices of DNA synthesis and sequencing
Every file address includes a true message and at least one false message, and the messages are distinguished via the hybridization to a truth marker oligonucleotide (Fig. 1b)

Summary

Introduction

The potential of DNA as an information storage medium is rapidly growing due to advances in DNA synthesis and sequencing. Conventional methods to destroy DNA include irradiating with ultraviolet light, using enzymes such as DNAse I8, applying high temperature of over 200 °C9,10, or using bleach[11] These DNA destruction methods vary in their approach, but are generally difficult to implement in decentralized settings without specialized equipment, and erasure may not always complete within a reasonable timeframe (Supplementary Note 6)[10,11]. We present a method of encoding information in DNA as a metastable aqueous solution that allows for rapid and permanent information erasure through a simple heating process (Fig. 1a). In our context, does not require destroying the potential messages by chemical degradation of DNA, but rather relies on the randomization of true/false flags encoded in hybridization state.

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